JAL-3253-applet JAL-3397

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 6f51420..1af23a4 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -35,8 +35,6 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
-import intervalstore.api.IntervalI;
-
 /**
  * A class that models a single contiguous feature on a sequence. If flag
  * 'contactFeature' is true, the start and end positions are interpreted instead
@@ -219,19 +217,22 @@ public class SequenceFeature implements FeatureLocationI
   @Override
   public boolean equals(Object o)
   {
-    return (o != null && (o instanceof SequenceFeature)
-            && equalsInterval((SequenceFeature) o));
+    return (o instanceof SequenceFeature
+            && equalsWithParent((SequenceFeature) o));
   }
 
   /**
-   * Having determined that this is in fact a SequenceFeature, now check it for
-   * equivalence. Overridden in CrossRef; used by IntervalStore (possibly).
+   * BH 2019.09.22 required due to subclassing by CrossRef and used by
+   * intervalstore.nonc.IntervalStoreImpl
+   * 
+   * @param sf
+   * @return
    */
-  @Override
-  public boolean equalsInterval(IntervalI sf)
+  public boolean equalsWithParent(SequenceFeature sf)
   {
-    return equals((SequenceFeature) sf, false);
+    return equals(sf, false);
   }
+
   /**
    * Overloaded method allows the equality test to optionally ignore the
    * 'Parent' attribute of a feature. This supports avoiding adding many
@@ -244,39 +245,17 @@ public class SequenceFeature implements FeatureLocationI
    */
   public boolean equals(SequenceFeature sf, boolean ignoreParent)
   {
-    boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
-            : score == sf.score;
-    if (begin != sf.begin || end != sf.end || !sameScore)
-    {
-      return false;
-    }
-
-    if (getStrand() != sf.getStrand())
-    {
-      return false;
-    }
-
-    if (!(type + description + featureGroup + getPhase()).equals(
-            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
-    {
-      return false;
-    }
-    if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
-    {
-      return false;
-    }
-    if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
-    {
-      return false;
-    }
-    if (!ignoreParent)
-    {
-      if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
-      {
-        return false;
-      }
-    }
-    return true;
+    return (begin == sf.begin && end == sf.end
+            && getStrand() == sf.getStrand()
+            && (Float.isNaN(score) ? Float.isNaN(sf.score)
+                    : score == sf.score)
+            && (type + description + featureGroup + getPhase())
+                    .equals(sf.type + sf.description + sf.featureGroup
+                            + sf.getPhase())
+            && equalAttribute(getValue("ID"), sf.getValue("ID"))
+            && equalAttribute(getValue("Name"), sf.getValue("Name"))
+            && (ignoreParent || equalAttribute(getValue("Parent"),
+                    sf.getValue("Parent"))));
   }
 
   /**